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NSF Bioinformatics Grants Awarded Aug. 1 — Sept. 11, 2008

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Biological Data Integration Using Large-Scale Molecular Interaction Networks. Start date: Aug. 1, 2008. Expires: July 31, 2009. Awarded amount to date: $593,873. Principal investigator: Trey Ideker. Sponsor: University of California-San Diego, Office of Contract and Grant Administration.
 
Funds a project to develop methods for mining biological interaction networks in order to “formulate models of cellular machinery and pathways,” according to the grant abstract. The investigators plan to focus on three areas of network integration: increasing the efficiency of pair-wise and multiple network alignment; protein-network-based diagnosis of disease, through classification of expression profiles gathered for use cases and controls; and alignment of physical interaction networks with expression quantitative trait loci interactions.
 

 
Similarity-Based Indexing and Integration of Protein Sequence and Structure Databases. Start date: Aug. 15, 2008. Expires: July 31, 2009. Awarded amount to date: $157,998. Principal investigator: Hakan Ferhatosmanoglu. Sponsor: Ohio State University Research Foundation.
 
Funds development of database indexing and similarity search technologies to manage, analyze, and integrate protein sequence and structure databases. The project will use a “unified theme” for both protein sequence and structure data, according to the grant abstract, based on “extracting key features and mapping them into compact feature vectors spaces to facilitate construction of integrated index structures with sensitive, accurate, and efficient querying capabilities,” the grant abstract states. For the sequence data, the project intends to develop feature-extraction methods that involve physiochemical properties of the amino acids and detect low level of similarities. For the structural data, the project will develop methods to capture local structural motifs using contact maps and spatial motifs. The software and the results of the project will be available here.
 

 
Automated Metabolic Reconstruction for All Sequenced Microbial Genomes. Start date: Aug. 15, 2008. Expires: July 31, 2009. Awarded amount to date: $70,889. Principal investigator: Matthew DeJongh. Sponsor: Hope College.
 
Supports an initiative to generate “substantially complete metabolic reconstructions for all sequenced microbial genomes,” according to the grant abstract. The approach involves an iterative process of identifying areas of metabolism encoded in microbial genomes that are not yet represented in public databases, creating new reaction network components for them, and generating updated metabolic reconstructions. The database of metabolic components and software will be fully integrated with the SEED comparative genome annotation and analysis environment, and the principal investigators will collaborate with the SEED community to disseminate the research results, the abstract states.
 

 
Database-Enabled Tools for Regulatory Metabolic Networks. Start date: Aug. 15, 2008. Expires: July 31, 2009. Awarded amount to date: $309,399. Principal investigator: Z. Meral Ozsoyoglu. Sponsor: Case Western Reserve University.
 
Supports the creation of a “database-enabled framework and tools” to aid model development for multiscale mechanistic models of biological systems. The set of tools, called PathCase-SB, will be able to link molecular information “to an understanding of how intact organisms function via multiscale mechanistic models of the system,” and “facilitate interactive model development and dynamic analysis of responses in an effective and efficient manner.” PathCase-SB will be “an add-on, and complementary,” to metabolic pathways data available in existing data sources, such as KEGG, Reactome, and BioCyc, the abstract states.
 

 
Acquisition of a Computer Cluster for Bioinformatics Research at UGA. Start date: Aug. 15, 2008. Expires: July 31, 2011. Awarded amount to date: $796,822. Principal investigator: Ying Xu. Sponsor: University of Georgia Research Foundation.
 
Funds the acquisition of a “high powered multiprocessor computer and a corresponding large disk storage capacity” at the University of Georgia. The system will be used to support the analysis and modeling of non-coding RNA genes, analysis and modeling of protein and carbohydrate structures, mining of eukaryotic and prokaryotic genomes, gene expression data analysis, and modeling of metabolic pathways and regulatory networks.
 

 
Utility and Usability of Text Mining for Biological Curation. Start date: Sept. 1, 2008. Expires: Aug. 31, 2010. Awarded amount to date: $199,259. Principal investigator: Lynette Hirschman. Sponsor: Mitre Corporation.
 
Supports a project that will evaluate a number of tools that are available for text mining and information extraction. The investigators “will work closely with database curators to assess the impact of the tools and develop evaluation methods to guide tool developers,” according to the grant abstract.
 

 
Graphs to Diversity: Extracting Genomic Variation from Sequence Graphs. Start date: Sept. 1, 2008. Expires: Aug. 31, 2010. Awarded amount to date: $293,074. Principal investigator: Mihai Pop. Sponsor: University of Maryland College Park.
 
Funds a project to develop a theoretical and computational infrastructure for studying genomic variation within mixtures of organisms. The project will rely on both theoretical and empirical analyses of the structure of genome assembly graphs in order to “characterize graph signatures that are correlated with intra- and inter- species polymorphisms,” according to the grant abstract. The investigators plan to place a “particular focus” on the information provided by next-generation sequencing technologies as well as other high-throughput experimental techniques.
 

 
Analysis of Mass Spectrometry Data for Biomarker Discovery. Start date: Sept. 1, 2008. Expires: Aug. 31, 2010. Awarded amount to date: $294,935. Principal investigator: Habtom Ressom. Sponsor: Georgetown University.
 
Supports a project to improve the analysis of mass spectrometry data for biomarker discovery. Goals of the project include investigating data-preprocessing algorithms for label-free quantification of peptides in serum using liquid chromatography/mass spectrometry, and investigating feature-selection algorithms that can isolate subgroup-specific biomarkers.
 

 
Algorithmic Strategies for Genotype-Phenotype Correlations. Start date: Sept. 1, 2008. Expires: Aug. 31, 2011. Awarded amount to date: $450,000. Principal investigator: Vineet Bafna. Sponsor: University of California-San Diego.
 
This project focuses on computational approaches to address “a subset of the problems that could arise in a typical whole-genome based association study,” according to the grant abstract. These problems include phasing of genotypes into haplotypes using overlapping sequence data and fast filtering for pairs of loci that interactively influence a phenotype and its application to multiple-locus testing of common disease phenotypes.
 

 
Adaptive Integration of Structured and Unstructured Data from Many Sources in a Biological Domain. Start date: Sept. 1, 2008. Expires: Aug. 31, 2011. Awarded amount to date: $443,128. Principal investigator: William Cohen. Sponsor: Carnegie-Mellon University.
 
Supports the development of a system “that learns to more accurately integrate the many heterogeneous sources of information that are relevant to a single scientist's research needs,” the grant abstract states. The system works by “loosely” integrating data of many different types, including unstructured text, into a single-typed directed graph, and then querying the graph using a query language that allows “schema-free similarity queries,” which specify a set of query terms and constraints on the desired output. The result of a query is a ranked list of entities that are ordered by similarity to the query terms. After a query, a user can label any of the suggested answers as “relevant” or “non-relevant” in order to drive a “learning phase” with the goal of producing a better ranking for future queries.
 

 
Acquisition of Computing Equipment for Research and Education in Computational Biology. Start date: Sept. 1, 2008. Expires: Aug. 31, 2011. Awarded amount to date: $256,086. Principal investigator: Amy Keating. Sponsor: Massachusetts Institute of Technology.
 
Funds the acquisition of “high-performance computing equipment for research and education in computational and systems biology,” according to the grant abstract. Projects planned for the computational system include the study of gene and organism evolution, transcriptional and post-transcriptional gene regulation, molecular signaling, protein conformational modeling, protein design, and the analysis of complex networks.
 

 
Mathematical Frameworks for Biological Modular Networks. Start date: Sept. 1, 2008. Expires: Aug. 31, 2011. Awarded amount to date: $523,333. Principal investigator: Hernan Makse. Sponsor: CUNY City College.
 
Supports a project that aims “to understand evolutionary principles by which biological networks have acquired their modular architecture, robustness, and preservation of diverse functions to sustain life,” according to the grant abstract. The investigators plan to address “the theme of emergent phenomena in biological complex networks with novel concepts from non-equilibrium systems and complexity, and to systematically transform these theoretical concepts into practically applicable models of functional modules.” In order to achieve this goal, the investigator will study functional modules by clustering and renormalization methods.
 

 
Modeling and Evolution of Biological Networks. Start date: Sept. 15, 2008. Expires: Aug. 31, 2010. Awarded amount to date: $210,000. Principal investigator: Eric Siggia. Sponsor: Cornell University.
 
Funds development of a “theoretical machinery” that predicts biological networks based on how rapidly they can be learned from random examples provided by mutation and selection. The approach “assumes the networks in living things can be built incrementally and grow continually by stepwise increases in fitness,” according to the grant abstract.
 

 
Integration of Bioinformatics into a Biology Curriculum. Start date: Dec. 1, 2008. Expires: Nov. 30, 2010. Awarded amount to date: $85,910. Principal investigator: Bruce Wightman. Sponsor: Muhlenberg College.
 
Supports an initiative at the Muhlenberg College departments of biology, chemistry, and mathematics and computer science to jointly integrate bioinformatics into biology and biochemistry courses at three levels: introductory, intermediate, and advanced. The project has two primary goals, according to the grant abstract: to improve undergraduate “sophistication” about bioinformatics; and to increase the mathematical content in the biology and biochemistry curricula.
 

 
Educational Assessment Tools for Genomics and Bioinformatics Education. Start date: Jan. 1, 2009. Expires: Dec. 31, 2011. This grant was awarded to two investigative teams:
  • Brian Morton. Sponsor: Barnard College. Awarded amount to date: $63,732.
  • Ross Nehm. Sponsor: Ohio State University Research Foundation. Awarded amount to date: $84,172.

Supports a project that aims to “assemble genomics and bioinformatics assessment items and tools into a single, freely-accessible, and user-friendly format,” according to the grant abstract. Among other goals, the project also plans to summarize validity and reliability data for existing measures and to construct a suite of supplemental genomics assessment tools in four areas: “knowledge, affect, performance, and faculty assessment.” The project team plans to “field test” its tools by using a newly developed interdisciplinary genomics curriculum at Barnard College as a test case.

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